Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes.

1. Cortez D, Marin R, Toledo-Flores D, Froidevaux L, Liechti A, Waters PD, Grützner F, Kaessmann H. Origins and functional evolution of Y chromosomes across mammals.. Nature 2014 Apr 24;508(7497):488-93.
   doi: 10.1038/nature13151pubmed: 24759410google scholar: lookup
2. Marshall Graves JA. Weird animal genomes and the evolution of vertebrate sex and sex chromosomes.. Annu Rev Genet 2008;42:565-86.
   doi: 10.1146/annurev.genet.42.110807.091714pubmed: 18983263google scholar: lookup
3. Lahn BT, Page DC. Four evolutionary strata on the human X chromosome.. Science 1999 Oct 29;286(5441):964-7.
   doi: 10.1126/science.286.5441.964pubmed: 10542153google scholar: lookup
4. Lahn BT, Page DC. Functional coherence of the human Y chromosome.. Science 1997 Oct 24;278(5338):675-80.
   doi: 10.1126/science.278.5338.675pubmed: 9381176google scholar: lookup
5. Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, Chinwalla A, Delehaunty A, Delehaunty K, Du H, Fewell G, Fulton L, Fulton R, Graves T, Hou SF, Latrielle P, Leonard S, Mardis E, Maupin R, McPherson J, Miner T, Nash W, Nguyen C, Ozersky P, Pepin K, Rock S, Rohlfing T, Scott K, Schultz B, Strong C, Tin-Wollam A, Yang SP, Waterston RH, Wilson RK, Rozen S, Page DC. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes.. Nature 2003 Jun 19;423(6942):825-37.
   doi: 10.1038/nature01722pubmed: 12815422google scholar: lookup
6. Hughes JF, Skaletsky H, Pyntikova T, Graves TA, van Daalen SK, Minx PJ, Fulton RS, McGrath SD, Locke DP, Friedman C, Trask BJ, Mardis ER, Warren WC, Repping S, Rozen S, Wilson RK, Page DC. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content.. Nature 2010 Jan 28;463(7280):536-9.
   doi: 10.1038/nature08700pmc: PMC3653425pubmed: 20072128google scholar: lookup
7. Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Graves T, Fulton RS, Dugan S, Ding Y, Buhay CJ, Kremitzki C, Wang Q, Shen H, Holder M, Villasana D, Nazareth LV, Cree A, Courtney L, Veizer J, Kotkiewicz H, Cho TJ, Koutseva N, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes.. Nature 2012 Feb 22;483(7387):82-6.
   doi: 10.1038/nature10843pmc: PMC3292678pubmed: 22367542google scholar: lookup
8. Hughes JF, Skaletsky H, Koutseva N, Pyntikova T, Page DC. Sex chromosome-to-autosome transposition events counter Y-chromosome gene loss in mammals.. Genome Biol 2015 May 28;16(1):104.
   doi: 10.1186/s13059-015-0667-4pmc: PMC4446799pubmed: 26017895google scholar: lookup
9. Hughes JF, Skaletsky H, Page DC. Sequencing of rhesus macaque Y chromosome clarifies origins and evolution of the DAZ (Deleted in AZoospermia) genes.. Bioessays 2012 Dec;34(12):1035-44.
   doi: 10.1002/bies.201200066pmc: PMC3581811pubmed: 23055411google scholar: lookup
10. Soh YQ, Alföldi J, Pyntikova T, Brown LG, Graves T, Minx PJ, Fulton RS, Kremitzki C, Koutseva N, Mueller JL, Rozen S, Hughes JF, Owens E, Womack JE, Murphy WJ, Cao Q, de Jong P, Warren WC, Wilson RK, Skaletsky H, Page DC. Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes.. Cell 2014 Nov 6;159(4):800-13.
    doi: 10.1016/j.cell.2014.09.052pmc: PMC4260969pubmed: 25417157google scholar: lookup
11. Tomaszkiewicz M, Rangavittal S, Cechova M, Campos Sanchez R, Fescemyer HW, Harris R, Ye D, O'Brien PC, Chikhi R, Ryder OA, Ferguson-Smith MA, Medvedev P, Makova KD. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y.. Genome Res 2016 Apr;26(4):530-40.
    doi: 10.1101/gr.199448.115pmc: PMC4817776pubmed: 26934921google scholar: lookup
12. Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho TJ, Koutseva N, Zaghlul S, Graves T, Rock S, Kremitzki C, Fulton RS, Dugan S, Ding Y, Morton D, Khan Z, Lewis L, Buhay C, Wang Q, Watt J, Holder M, Lee S, Nazareth L, Alföldi J, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators.. Nature 2014 Apr 24;508(7497):494-9.
    doi: 10.1038/nature13206pmc: PMC4139287pubmed: 24759411google scholar: lookup
13. Li G, Davis BW, Raudsepp T, Pearks Wilkerson AJ, Mason VC, Ferguson-Smith M, O'Brien PC, Waters PD, Murphy WJ. Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution.. Genome Res 2013 Sep;23(9):1486-95.
    doi: 10.1101/gr.154286.112pmc: PMC3759724pubmed: 23788650google scholar: lookup
14. Skinner BM, Sargent CA, Churcher C, Hunt T, Herrero J, Loveland JE, Dunn M, Louzada S, Fu B, Chow W, Gilbert J, Austin-Guest S, Beal K, Carvalho-Silva D, Cheng W, Gordon D, Grafham D, Hardy M, Harley J, Hauser H, Howden P, Howe K, Lachani K, Ellis PJ, Kelly D, Kerry G, Kerwin J, Ng BL, Threadgold G, Wileman T, Wood JM, Yang F, Harrow J, Affara NA, Tyler-Smith C. The pig X and Y Chromosomes: structure, sequence, and evolution.. Genome Res 2016 Jan;26(1):130-9.
    doi: 10.1101/gr.188839.114pmc: PMC4691746pubmed: 26560630google scholar: lookup
15. Hughes JF, Page DC. The Biology and Evolution of Mammalian Y Chromosomes.. Annu Rev Genet 2015;49:507-27.
    doi: 10.1146/annurev-genet-112414-055311pubmed: 26442847google scholar: lookup
16. Hughes JF, Page DC. The history of the Y chromosome in man.. Nat Genet 2016 May 27;48(6):588-9.
    doi: 10.1038/ng.3580pubmed: 27230683google scholar: lookup
17. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MC, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Lander ES, Lindblad-Toh K. Genome sequence, comparative analysis, and population genetics of the domestic horse.. Science 2009 Nov 6;326(5954):865-7.
    doi: 10.1126/science.1178158pmc: PMC3785132pubmed: 19892987google scholar: lookup
18. Paria N, Raudsepp T, Pearks Wilkerson AJ, O'Brien PC, Ferguson-Smith MA, Love CC, Arnold C, Rakestraw P, Murphy WJ, Chowdhary BP. A gene catalogue of the euchromatic male-specific region of the horse Y chromosome: comparison with human and other mammals.. PLoS One 2011;6(7):e21374.
    doi: 10.1371/journal.pone.0021374pmc: PMC3143126pubmed: 21799735google scholar: lookup
19. Wallner B, Palmieri N, Vogl C, Rigler D, Bozlak E, Druml T, Jagannathan V, Leeb T, Fries R, Tetens J, Thaller G, Metzger J, Distl O, Lindgren G, Rubin CJ, Andersson L, Schaefer R, McCue M, Neuditschko M, Rieder S, Schlötterer C, Brem G. Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions.. Curr Biol 2017 Jul 10;27(13):2029-2035.e5.
    doi: 10.1016/j.cub.2017.05.086pubmed: 28669755google scholar: lookup
20. Bowling AT, Breen M, Chowdhary BP, Hirota K, Lear T, Millon LV, Ponce de Leon FA, Raudsepp T, Stranzinger G. International system for cytogenetic nomenclature of the domestic horse. Report of the Third International Committee for the Standardization of the domestic horse karyotype, Davis, CA, USA, 1996.. Chromosome Res 1997 Nov;5(7):433-43.
    pubmed: 9421259doi: 10.1023/a:1018408811881google scholar: lookup
21. Raudsepp T, Chowdhary BP. The horse pseudoautosomal region (PAR): characterization and comparison with the human, chimp and mouse PARs.. Cytogenet Genome Res 2008;121(2):102-9.
    doi: 10.1159/000125835pubmed: 18544933google scholar: lookup
22. Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L. Speciation with gene flow in equids despite extensive chromosomal plasticity.. Proc Natl Acad Sci U S A 2014 Dec 30;111(52):18655-60.
    doi: 10.1073/pnas.1412627111pmc: PMC4284605pubmed: 25453089google scholar: lookup
23. Raudsepp T, Durkin K, Lear TL, Das PJ, Avila F, Kachroo P, Chowdhary BP. Molecular heterogeneity of XY sex reversal in horses.. Anim Genet 2010 Dec;41 Suppl 2:41-52.
    doi: 10.1111/j.1365-2052.2010.02101.xpubmed: 21070275google scholar: lookup
24. Murphy WJ, Pearks Wilkerson AJ, Raudsepp T, Agarwala R, Schäffer AA, Stanyon R, Chowdhary BP. Novel gene acquisition on carnivore Y chromosomes.. PLoS Genet 2006 Mar;2(3):e43.
    doi: 10.1371/journal.pgen.0020043pmc: PMC1420679pubmed: 16596168google scholar: lookup
25. Raudsepp T, Chowdhary BP. The Eutherian Pseudoautosomal Region.. Cytogenet Genome Res 2015;147(2-3):81-94.
    doi: 10.1159/000443157pubmed: 26730606google scholar: lookup
26. Skinner BM, Lachani K, Sargent CA, Yang F, Ellis P, Hunt T, Fu B, Louzada S, Churcher C, Tyler-Smith C, Affara NA. Expansion of the HSFY gene family in pig lineages : HSFY expansion in suids.. BMC Genomics 2015 Jun 9;16(1):442.
    doi: 10.1186/s12864-015-1650-xpmc: PMC4460688pubmed: 26055083google scholar: lookup
27. Lange J, Skaletsky H, van Daalen SK, Embry SL, Korver CM, Brown LG, Oates RD, Silber S, Repping S, Page DC. Isodicentric Y chromosomes and sex disorders as byproducts of homologous recombination that maintains palindromes.. Cell 2009 Sep 4;138(5):855-69.
    doi: 10.1016/j.cell.2009.07.042pmc: PMC3616640pubmed: 19737515google scholar: lookup
28. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. The evolution of lncRNA repertoires and expression patterns in tetrapods.. Nature 2014 Jan 30;505(7485):635-40.
    doi: 10.1038/nature12943pubmed: 24463510google scholar: lookup
29. Steiner CC, Ryder OA. Molecular phylogeny and evolution of the Perissodactyla. Zool. J. Linn. Soc. 2011;163:1289–1303.
    doi: 10.1111/j.1096-3642.2011.00752.xgoogle scholar: lookup
30. Nielsen MK, Wang J, Davis R, Bellaw JL, Lyons ET, Lear TL, Goday C. Parascaris univalens--a victim of large-scale misidentification?. Parasitol Res 2014 Dec;113(12):4485-90.
    doi: 10.1007/s00436-014-4135-ypubmed: 25231078google scholar: lookup
31. Soumillon M, Necsulea A, Weier M, Brawand D, Zhang X, Gu H, Barthès P, Kokkinaki M, Nef S, Gnirke A, Dym M, de Massy B, Mikkelsen TS, Kaessmann H. Cellular source and mechanisms of high transcriptome complexity in the mammalian testis.. Cell Rep 2013 Jun 27;3(6):2179-90.
    doi: 10.1016/j.celrep.2013.05.031pubmed: 23791531google scholar: lookup
32. Ivancevic AM, Walsh AM, Kortschak RD, Adelson DL. Jumping the fine LINE between species: horizontal transfer of transposable elements in animals catalyses genome evolution.. Bioessays 2013 Dec;35(12):1071-82.
    doi: 10.1002/bies.201300072pubmed: 24003001google scholar: lookup
33. Walsh AM, Kortschak RD, Gardner MG, Bertozzi T, Adelson DL. Widespread horizontal transfer of retrotransposons.. Proc Natl Acad Sci U S A 2013 Jan 15;110(3):1012-6.
    doi: 10.1073/pnas.1205856110pmc: PMC3549140pubmed: 23277587google scholar: lookup
34. Suh A, Witt CC, Menger J, Sadanandan KR, Podsiadlowski L, Gerth M, Weigert A, McGuire JA, Mudge J, Edwards SV, Rheindt FE. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes.. Nat Commun 2016 Apr 21;7:11396.
    doi: 10.1038/ncomms11396pmc: PMC4844689pubmed: 27097561google scholar: lookup
35. Wijayawardena BK, Minchella DJ, DeWoody JA. Horizontal gene transfer in schistosomes: A critical assessment.. Mol Biochem Parasitol 2015 May;201(1):57-65.
    doi: 10.1016/j.molbiopara.2015.05.008pubmed: 26048565google scholar: lookup
36. Repping S, Skaletsky H, Lange J, Silber S, Van Der Veen F, Oates RD, Page DC, Rozen S. Recombination between palindromes P5 and P1 on the human Y chromosome causes massive deletions and spermatogenic failure.. Am J Hum Genet 2002 Oct;71(4):906-22.
    doi: 10.1086/342928pmc: PMC419997pubmed: 12297986google scholar: lookup
37. Grzmil P, Gołas A, Müller C, Styrna J. The influence of the deletion on the long arm of the Y chromosome on sperm motility in mice.. Theriogenology 2007 Mar 1;67(4):760-6.
    doi: 10.1016/j.theriogenology.2006.10.007pubmed: 17126391google scholar: lookup
38. Yamauchi Y, Riel JM, Stoytcheva Z, Burgoyne PS, Ward MA. Deficiency in mouse Y chromosome long arm gene complement is associated with sperm DNA damage.. Genome Biol 2010;11(6):R66.
    doi: 10.1186/gb-2010-11-6-r66pmc: PMC2911114pubmed: 20573212google scholar: lookup
39. Ellis PJ, Clemente EJ, Ball P, Touré A, Ferguson L, Turner JM, Loveland KL, Affara NA, Burgoyne PS. Deletions on mouse Yq lead to upregulation of multiple X- and Y-linked transcripts in spermatids.. Hum Mol Genet 2005 Sep 15;14(18):2705-15.
    doi: 10.1093/hmg/ddi304pubmed: 16087683google scholar: lookup
40. Steiner CC, Ryder OA. Characterization of Prdm9 in equids and sterility in mules.. PLoS One 2013;8(4):e61746.
    doi: 10.1371/journal.pone.0061746pmc: PMC3632555pubmed: 23613924google scholar: lookup
41. Chandley AC, Jones RC, Dott HM, Allen WR, Short RV. Meiosis in interspecific equine hybrids. I. The male mule (Equus asinus X E. caballus) and hinny (E. caballus X E. asinus).. Cytogenet Cell Genet 1974;13(4):330-41.
    doi: 10.1159/000130284pubmed: 4430187google scholar: lookup
42. Civetta A. Misregulation of Gene Expression and Sterility in Interspecies Hybrids: Causal Links and Alternative Hypotheses.. J Mol Evol 2016 May;82(4-5):176-82.
    doi: 10.1007/s00239-016-9734-zpubmed: 27025762google scholar: lookup
43. Tessari A, Salata E, Ferlin A, Bartoloni L, Slongo ML, Foresta C. Characterization of HSFY, a novel AZFb gene on the Y chromosome with a possible role in human spermatogenesis.. Mol Hum Reprod 2004 Apr;10(4):253-8.
    doi: 10.1093/molehr/gah036pubmed: 14985478google scholar: lookup
44. Cocquet J, Ellis PJ, Mahadevaiah SK, Affara NA, Vaiman D, Burgoyne PS. A genetic basis for a postmeiotic X versus Y chromosome intragenomic conflict in the mouse.. PLoS Genet 2012 Sep;8(9):e1002900.
    doi: 10.1371/journal.pgen.1002900pmc: PMC3441658pubmed: 23028340google scholar: lookup
45. Lindgren G, Backström N, Swinburne J, Hellborg L, Einarsson A, Sandberg K, Cothran G, Vilà C, Binns M, Ellegren H. Limited number of patrilines in horse domestication.. Nat Genet 2004 Apr;36(4):335-6.
    doi: 10.1038/ng1326pubmed: 15034578google scholar: lookup
46. Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover CA, Lorente-Galdos B, Nedoluzhko A, Boulygina E, Tsygankova S, Neuditschko M, Jagannathan V, Thèves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Sicheritz-Ponten T, Popov R, Grigoriev S, Alekseev AN, Rubin EM, McCue M, Rieder S, Leeb T, Tikhonov A, Crubézy E, Slatkin M, Marques-Bonet T, Nielsen R, Willerslev E, Kantanen J, Prokhortchouk E, Orlando L. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.. Proc Natl Acad Sci U S A 2015 Dec 15;112(50):E6889-97.
    doi: 10.1073/pnas.1513696112pmc: PMC4687531pubmed: 26598656google scholar: lookup
47. Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M, Seguin-Orlando A, Korneliussen TS, Velazquez AM, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, MacHugh DE, Kalbfleisch T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MT, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L. Prehistoric genomes reveal the genetic foundation and cost of horse domestication.. Proc Natl Acad Sci U S A 2014 Dec 30;111(52):E5661-9.
    doi: 10.1073/pnas.1416991111pmc: PMC4284583pubmed: 25512547google scholar: lookup
48. Lippold S, Knapp M, Kuznetsova T, Leonard JA, Benecke N, Ludwig A, Rasmussen M, Cooper A, Weinstock J, Willerslev E, Shapiro B, Hofreiter M. Discovery of lost diversity of paternal horse lineages using ancient DNA.. Nat Commun 2011 Aug 23;2:450.
    doi: 10.1038/ncomms1447pubmed: 21863017google scholar: lookup
49. Wallner B, Piumi F, Brem G, Müller M, Achmann R. Isolation of Y chromosome-specific microsatellites in the horse and cross-species amplification in the genus Equus.. J Hered 2004 Mar-Apr;95(2):158-64.
    doi: 10.1093/jhered/esh020pubmed: 15073232google scholar: lookup
50. Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.. Nature 2013 Jul 4;499(7456):74-8.
    doi: 10.1038/nature12323pubmed: 23803765google scholar: lookup
51. Raudsepp T, Santani A, Wallner B, Kata SR, Ren C, Zhang HB, Womack JE, Skow LC, Chowdhary BP. A detailed physical map of the horse Y chromosome.. Proc Natl Acad Sci U S A 2004 Jun 22;101(25):9321-6.
    doi: 10.1073/pnas.0403011101pmc: PMC438975pubmed: 15197257google scholar: lookup
52. Raudsepp T, Chowdhary BP. FISH for mapping single copy genes.. Methods Mol Biol 2008;422:31-49.
    doi: 10.1007/978-1-59745-581-7_3pubmed: 18629659google scholar: lookup
53. Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. Primer3--new capabilities and interfaces.. Nucleic Acids Res 2012 Aug;40(15):e115.
    doi: 10.1093/nar/gks596pmc: PMC3424584pubmed: 22730293google scholar: lookup
54. Milenkovic D, Oustry-Vaiman A, Lear TL, Billault A, Mariat D, Piumi F, Schibler L, Cribiu E, Guérin G. Cytogenetic localization of 136 genes in the horse: comparative mapping with the human genome.. Mamm Genome 2002 Sep;13(9):524-34.
    doi: 10.1007/s00335-001-2137-4pubmed: 12370783google scholar: lookup
55. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs.. Genome Res 2008 May;18(5):821-9.
    doi: 10.1101/gr.074492.107pmc: PMC2336801pubmed: 18349386google scholar: lookup
56. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements.. Genome Res 2004 Jul;14(7):1394-403.
    doi: 10.1101/gr.2289704pmc: PMC442156pubmed: 15231754google scholar: lookup
57. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.. Nat Protoc 2013 Aug;8(8):1494-512.
    doi: 10.1038/nprot.2013.084pmc: PMC3875132pubmed: 23845962google scholar: lookup
58. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.. Genome Res 2008 Jan;18(1):188-96.
    doi: 10.1101/gr.6743907pmc: PMC2134774pubmed: 18025269google scholar: lookup
59. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner.. Bioinformatics 2013 Jan 1;29(1):15-21.
    doi: 10.1093/bioinformatics/bts635pmc: PMC3530905pubmed: 23104886google scholar: lookup
60. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity.. BMC Bioinformatics 2004 Aug 19;5:113.
    doi: 10.1186/1471-2105-5-113pmc: PMC517706pubmed: 15318951google scholar: lookup
61. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.. Bioinformatics 2014 May 1;30(9):1312-3.
    doi: 10.1093/bioinformatics/btu033pmc: PMC3998144pubmed: 24451623google scholar: lookup
62. Hedges SB, Marin J, Suleski M, Paymer M, Kumar S. Tree of life reveals clock-like speciation and diversification.. Mol Biol Evol 2015 Apr;32(4):835-45.
    doi: 10.1093/molbev/msv037pmc: PMC4379413pubmed: 25739733google scholar: lookup
63. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood.. Mol Biol Evol 2007 Aug;24(8):1586-91.
    doi: 10.1093/molbev/msm088pubmed: 17483113google scholar: lookup
64. Li WH. Unbiased estimation of the rates of synonymous and nonsynonymous substitution.. J Mol Evol 1993 Jan;36(1):96-9.
    doi: 10.1007/BF02407308pubmed: 8433381google scholar: lookup
65. Sawyer S. Statistical tests for detecting gene conversion.. Mol Biol Evol 1989 Sep;6(5):526-38.
    pubmed: 2677599doi: 10.1093/oxfordjournals.molbev.a040567google scholar: lookup
66. Das PJ, Mishra DK, Ghosh S, Avila F, Johnson GA, Chowdhary BP, Raudsepp T. Comparative organization and gene expression profiles of the porcine pseudoautosomal region.. Cytogenet Genome Res 2013;141(1):26-36.
    doi: 10.1159/000351310pubmed: 23735614google scholar: lookup
67. Das PJ, Chowdhary BP, Raudsepp T. Characterization of the bovine pseudoautosomal region and comparison with sheep, goat, and other mammalian pseudoautosomal regions.. Cytogenet Genome Res 2009;126(1-2):139-47.
    doi: 10.1159/000245913pubmed: 20016163google scholar: lookup
68. Das PJ, Lyle SK, Beehan D, Chowdhary BP, Raudsepp T. Cytogenetic and molecular characterization of Y isochromosome in a 63XO/64Xi(Yq) mosaic karyotype of an intersex horse.. Sex Dev 2012;6(1-3):117-27.
    doi: 10.1159/000332212pubmed: 22005008google scholar: lookup

Citations

1. Giontella A, Cardinali I, Sarti FM, Silvestrelli M, Lancioni H. Y-Chromosome Haplotype Report among Eight Italian Horse Breeds.. Genes (Basel) 2023 Aug 9;14(8).
   doi: 10.3390/genes14081602pubmed: 37628653google scholar: lookup
2. Kaufmann P, Wiberg RAW, Papachristos K, Scofield DG, Tellgren-Roth C, Immonen E. Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles.. Mol Biol Evol 2023 Aug 3;40(8).
   doi: 10.1093/molbev/msad167pubmed: 37479678google scholar: lookup
3. Batcher K, Varney S, Raudsepp T, Jevit M, Dickinson P, Jagannathan V, Leeb T, Bannasch D. Ancient segmentally duplicated LCORL retrocopies in equids.. PLoS One 2023;18(6):e0286861.
   doi: 10.1371/journal.pone.0286861pubmed: 37289743google scholar: lookup
4. Gong Y, Li Y, Liu X, Ma Y, Jiang L. A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?. J Anim Sci Biotechnol 2023 May 5;14(1):73.
   doi: 10.1186/s40104-023-00860-1pubmed: 37143156google scholar: lookup
5. Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity.. Genes (Basel) 2022 Dec 2;13(12).
   doi: 10.3390/genes13122272pubmed: 36553539google scholar: lookup
6. Castaneda C, Radović L, Felkel S, Juras R, Davis BW, Cothran EG, Wallner B, Raudsepp T. Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups.. G3 (Bethesda) 2022 Dec 1;12(12).
   doi: 10.1093/g3journal/jkac278pubmed: 36227030google scholar: lookup
7. Pei S, Xu H, Wang L, Li F, Li W, Yue X. Copy number variation of ZNF280BY across eight sheep breeds and its association with testicular size of Hu sheep.. J Anim Sci 2022 Sep 1;100(9).
   doi: 10.1093/jas/skac232pubmed: 35775620google scholar: lookup
8. Ghosh S, Kjöllerström J, Metcalfe L, Reed S, Juras R, Raudsepp T. The Second Case of Non-Mosaic Trisomy of Chromosome 26 with Homologous Fusion 26q;26q in the Horse.. Animals (Basel) 2022 Mar 22;12(7).
   doi: 10.3390/ani12070803pubmed: 35405793google scholar: lookup
9. Rossetti C, Genualdo V, Incarnato D, Mottola F, Perucatti A, Pauciullo A. State of the art on the physical mapping of the Y-chromosome in the Bovidae and comparison with other species - A review.. Anim Biosci 2022 Sep;35(9):1289-1302.
   doi: 10.5713/ab.21.0480pubmed: 35240029google scholar: lookup
10. Castaneda C, Ruiz AJ, Tibary A, Raudsepp T. Molecular Cytogenetic and Y Copy Number Analysis of a Reciprocal ECAY-ECA13 Translocation in a Stallion with Complete Meiotic Arrest.. Genes (Basel) 2021 Nov 26;12(12).
    doi: 10.3390/genes12121892pubmed: 34946841google scholar: lookup
11. Akter R, El-Hage CM, Sansom FM, Carrick J, Devlin JM, Legione AR. Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses.. BMC Genomics 2021 Oct 2;22(1):713.
    doi: 10.1186/s12864-021-08010-5pubmed: 34600470google scholar: lookup
12. Li R, Yang P, Dai X, Asadollahpour Nanaei H, Fang W, Yang Z, Cai Y, Zheng Z, Wang X, Jiang Y. A near complete genome for goat genetic and genomic research.. Genet Sel Evol 2021 Sep 10;53(1):74.
    doi: 10.1186/s12711-021-00668-5pubmed: 34507524google scholar: lookup
13. Naftaly AS, Pau S, White MA. Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish.. Genome Res 2021 Aug;31(8):1486-1497.
    doi: 10.1101/gr.274282.120pubmed: 34131005google scholar: lookup
14. Bugno-Poniewierska M, Raudsepp T. Horse Clinical Cytogenetics: Recurrent Themes and Novel Findings.. Animals (Basel) 2021 Mar 16;11(3).
    doi: 10.3390/ani11030831pubmed: 33809432google scholar: lookup
15. Rabinowitz MJ, Huffman PJ, Haney NM, Kohn TP. Y-Chromosome Microdeletions: A Review of Prevalence, Screening, and Clinical Considerations.. Appl Clin Genet 2021;14:51-59.
    doi: 10.2147/TACG.S267421pubmed: 33603438google scholar: lookup
16. Bellott DW, Page DC. Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals.. Genome Res 2021 Jan 21;31(2):198-210.
    doi: 10.1101/gr.268516.120pubmed: 33479023google scholar: lookup
17. Jevit MJ, Davis BW, Castaneda C, Hillhouse A, Juras R, Trifonov VA, Tibary A, Pereira JC, Ferguson-Smith MA, Raudsepp T. An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome.. Genes (Basel) 2021 Jan 16;12(1).
    doi: 10.3390/genes12010105pubmed: 33467186google scholar: lookup
18. Wang C, Li H, Guo Y, Huang J, Sun Y, Min J, Wang J, Fang X, Zhao Z, Wang S, Zhang Y, Liu Q, Jiang Q, Wang X, Guo Y, Yang C, Wang Y, Tian F, Zhuang G, Fan Y, Gao Q, Li Y, Ju Z, Li J, Li R, Hou M, Yang G, Liu G, Liu W, Guo J, Pan S, Fan G, Zhang W, Zhang R, Yu J, Zhang X, Yin Q, Ji C, Jin Y, Yue G, Liu M, Xu J, Liu S, Jordana J, Noce A, Amills M, Wu DD, Li S, Zhou X, Zhong J. Donkey genomes provide new insights into domestication and selection for coat color.. Nat Commun 2020 Dec 8;11(1):6014.
    doi: 10.1038/s41467-020-19813-7pubmed: 33293529google scholar: lookup
19. Hughes JF, Skaletsky H, Pyntikova T, Koutseva N, Raudsepp T, Brown LG, Bellott DW, Cho TJ, Dugan-Rocha S, Khan Z, Kremitzki C, Fronick C, Graves-Lindsay TA, Fulton L, Warren WC, Wilson RK, Owens E, Womack JE, Murphy WJ, Muzny DM, Worley KC, Chowdhary BP, Gibbs RA, Page DC. Sequence analysis in Bos taurus reveals pervasiveness of X-Y arms races in mammalian lineages.. Genome Res 2020 Dec;30(12):1716-1726.
    doi: 10.1101/gr.269902.120pubmed: 33208454google scholar: lookup
20. Xu L, Irestedt M, Zhou Q. Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds.. Genes (Basel) 2020 Oct 28;11(11).
    doi: 10.3390/genes11111267pubmed: 33126459google scholar: lookup
21. Li R, Yang P, Li M, Fang W, Yue X, Nanaei HA, Gan S, Du D, Cai Y, Dai X, Yang Q, Cao C, Deng W, He S, Li W, Ma R, Liu M, Jiang Y. A Hu sheep genome with the first ovine Y chromosome reveal introgression history after sheep domestication.. Sci China Life Sci 2021 Jul;64(7):1116-1130.
    doi: 10.1007/s11427-020-1807-0pubmed: 32997330google scholar: lookup
22. Martínez-Pacheco M, Tenorio M, Almonte L, Fajardo V, Godínez A, Fernández D, Cornejo-Páramo P, Díaz-Barba K, Halbert J, Liechti A, Székely T, Urrutia AO, Cortez D. Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals.. Genome Biol Evol 2020 Nov 3;12(11):2015-2028.
    doi: 10.1093/gbe/evaa173pubmed: 32790864google scholar: lookup
23. Peichel CL, McCann SR, Ross JA, Naftaly AFS, Urton JR, Cech JN, Grimwood J, Schmutz J, Myers RM, Kingsley DM, White MA. Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution.. Genome Biol 2020 Jul 19;21(1):177.
    doi: 10.1186/s13059-020-02097-xpubmed: 32684159google scholar: lookup
24. Moretti C, Blanco M, Ialy-Radio C, Serrentino ME, Gobé C, Friedman R, Battail C, Leduc M, Ward MA, Vaiman D, Tores F, Cocquet J. Battle of the Sex Chromosomes: Competition between X and Y Chromosome-Encoded Proteins for Partner Interaction and Chromatin Occupancy Drives Multicopy Gene Expression and Evolution in Muroid Rodents.. Mol Biol Evol 2020 Dec 16;37(12):3453-3468.
    doi: 10.1093/molbev/msaa175pubmed: 32658962google scholar: lookup
25. Liu S, Yang Y, Pan Q, Sun Y, Ma H, Liu Y, Wang M, Zhao C, Wu C. Ancient Patrilineal Lines and Relatively High ECAY Diversity Preserved in Indigenous Horses Revealed With Novel Y-Chromosome Markers.. Front Genet 2020;11:467.
    doi: 10.3389/fgene.2020.00467pubmed: 32508879google scholar: lookup
26. Mendoza MN, Raudsepp T, More MJ, Gutiérrez GA, Ponce de León FA. Cytogenetic Mapping of 35 New Markers in the Alpaca (Vicugna pacos).. Genes (Basel) 2020 May 8;11(5).
    doi: 10.3390/genes11050522pubmed: 32397072google scholar: lookup
27. Liu R, Low WY, Tearle R, Koren S, Ghurye J, Rhie A, Phillippy AM, Rosen BD, Bickhart DM, Smith TPL, Hiendleder S, Williams JL. New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes.. BMC Genomics 2019 Dec 19;20(1):1000.
    doi: 10.1186/s12864-019-6364-zpubmed: 31856728google scholar: lookup
28. Kruger AN, Brogley MA, Huizinga JL, Kidd JM, de Rooij DG, Hu YC, Mueller JL. A Neofunctionalized X-Linked Ampliconic Gene Family Is Essential for Male Fertility and Equal Sex Ratio in Mice.. Curr Biol 2019 Nov 4;29(21):3699-3706.e5.
    doi: 10.1016/j.cub.2019.08.057pubmed: 31630956google scholar: lookup
29. Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era.. Anim Genet 2019 Dec;50(6):569-597.
    doi: 10.1111/age.12857pubmed: 31568563google scholar: lookup
30. Acosta A, Suárez-Varón G, Rodríguez-Miranda LA, Lira-Noriega A, Aguilar-Gómez D, Gutiérrez-Mariscal M, Hernández-Gallegos O, Méndez-de-la-Cruz F, Cortez D. Corytophanids Replaced the Pleurodont XY System with a New Pair of XY Chromosomes.. Genome Biol Evol 2019 Sep 1;11(9):2666-2677.
    doi: 10.1093/gbe/evz196pubmed: 31557287google scholar: lookup
31. Rando HM, Wadlington WH, Johnson JL, Stutchman JT, Trut LN, Farré M, Kukekova AV. The Red Fox Y-Chromosome in Comparative Context.. Genes (Basel) 2019 May 28;10(6).
    doi: 10.3390/genes10060409pubmed: 31142040google scholar: lookup
32. Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, Rubin CJ, Schaefer R, Schlötterer C, Thaller G, Tetens J, Velie B, Brem G, Wallner B. The horse Y chromosome as an informative marker for tracing sire lines.. Sci Rep 2019 Apr 15;9(1):6095.
    doi: 10.1038/s41598-019-42640-wpubmed: 30988347google scholar: lookup
33. Kim SW, Jo A, Im J, Lee HE, Kim HS. Expression analysis of miR-221-3p and its target genes in horses.. Genes Genomics 2019 Apr;41(4):459-465.
    doi: 10.1007/s13258-018-00778-3pubmed: 30604147google scholar: lookup